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  • Relative Free Energies from Non-Equilibrium Simulations: Application to Changes in Density

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    Davie_2014_02Thesis.pdf (1.458Mb)
    Author(s)
    Davie, Stuart J.
    Primary Supervisor
    Bernhardt, Debra
    Other Supervisors
    Jepps, Owen
    Year published
    2014
    Metadata
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    Abstract
    Knowledge of free-energy differences for states of a system provides an essential component in understanding many processes, including solubility, reaction rates, and phase changes. Therefore, the development of efficient, accurate free-energy calculation routines has long been of interest within the field of molecular modelling. Until recently, thermodynamic integration, free-energy perturbation and slow-change techniques were the only approaches available for the calculation of free-energy differences between two states of a system. However, with the discovery of non-equilibrium free-energy relations in the late nineties, ...
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    Knowledge of free-energy differences for states of a system provides an essential component in understanding many processes, including solubility, reaction rates, and phase changes. Therefore, the development of efficient, accurate free-energy calculation routines has long been of interest within the field of molecular modelling. Until recently, thermodynamic integration, free-energy perturbation and slow-change techniques were the only approaches available for the calculation of free-energy differences between two states of a system. However, with the discovery of non-equilibrium free-energy relations in the late nineties, new calculation approaches are now possible. This thesis demonstrates the application of these new relations by deriving them from statistical mechanical concepts and applying them to a variety of systems. Although other types of systems are considered, the focus of this work is on the investigation of density changes, as the density of a system is one of its fundamental intrinsic properties, and expansion and compression phenomena are central to many thermodynamic investigations. To investigate the convergence properties of the free-energy calculation methods prior to their application to systems undergoing a density change, a novel transformation between Lennard-Jones systems possessing different potentials is developed and simulations are completed for a variety of transformation parameters. In particular, the accuracy of free-energy calculations as a function of transformation rate is considered, along with a detailed analysis of free-energy convergence as a function of the number of transformations completed.
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    Thesis Type
    Thesis (PhD Doctorate)
    Degree Program
    Doctor of Philosophy (PhD)
    School
    School of Biomolecular and Physical Sciences
    DOI
    https://doi.org/10.25904/1912/403
    Copyright Statement
    The author owns the copyright in this thesis, unless stated otherwise.
    Item Access Status
    Public
    Note
    In order to comply with copyright Chapters 6, 7 an 8 have not been published here.
    Subject
    Thermodynamic integration
    Free-energy perturbation
    Slow-change techniques
    Free-energy differences
    Non-Equilibrium Simulations
    Lennard-Jones systems
    Free-energy calculation methods
    Publication URI
    http://hdl.handle.net/10072/365922
    Collection
    • Theses - Higher Degree by Research

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